Real, chasing a record-extending 10th title, beat visitors Khimki Moscow 83-70, while Barcelona produced a steely defensive performance in a 66-59 win at 1999 champions Zalgiris Kaunas.
The defending champions will face Fenerbahce Istanbul in the playoffs, with the Turkish side having home court advantage in the best-of-five quarter-final series.
Barca meet Lokomotiv Krasnodar, Panathinaikos face Laboral Kutxa Vitoria and CSKA Moscow lock horns with Red Star Belgrade in the opening games of the other three match-ups next week.
The winners advance to the May 13-15 Final Four in Berlin.
Real, who were staring at the possibility of an early exit after patchy performances throughout the two group stages, showed their class when they needed it most.
The holders repelled a fierce Khimki onslaught in an electrifying first half and led 54-49, with shooting guard Jaycee Carroll scoring 16 points and 36-year old centre Felipe Reyes adding 15 in the opening period.
TORRID PACE
They cancelled out a brilliant individual effort from Khimki playmaker Tyrese Rice, who chalked up 22 points through the first two quarters as he nailed nine of 10 shots.
The torrid pace took its toll as both teams started to struggle in offence in the third period before Real pulled away in the final quarter to the delight of the home fans.
"It was an unbelievably tough group and it was very difficult for us but I am very happy that we were able to go through in the final game," Real coach Pablo Laso told Euroleague television.
Carroll finished on 23 points and Reyes chipped in with 18, while Rice had a quiet second half, scoring just two points to reach a total of 24.
Barcelona guard Pau Ribas was instrumental in their success, netting all of his 14 points in the second half as the Catalan side overturned a 34-28 halftime deficit in Lithuania.
Ribas nailed all his four shots from three-point range while centre Joey Dorsey added 12 points and 13 rebounds, despite hitting only two of nine free throws.
"I was upset with myself for missing a lot of free throws but fortunately we came away with a win because we played hard," said Dorsey. "We made some big shots in the second half."
(Editing by Ken Ferris)
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